Contacts of the helix formed by residues 287 - 301 (chain D) in PDB entry 1SEJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 287 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285D LYS 4.2 1.0 + - - -
286D VAL* 1.3 71.5 - - - +
288D ILE* 1.3 65.4 + - - +
289D ARG* 3.3 3.1 + - + +
290D SER* 3.5 21.7 + - - +
291D ILE* 3.3 24.9 + - - +
433D PHE* 3.9 12.2 - - + -
616D F89 4.6 11.8 + - - +
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Residues in contact with ILE 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D PHE* 4.0 22.9 - - + -
280D LEU* 4.5 6.3 - - + -
286D VAL 3.0 10.2 + - - +
287D ALA* 1.3 70.0 - - - +
289D ARG* 1.3 69.2 + - - +
291D ILE* 3.1 20.7 + - + +
292D PHE* 2.9 20.4 + - - +
440D ILE* 3.7 27.6 - - + -
487D LEU* 4.7 9.2 - - + -
501D TRP* 3.5 26.5 - - + -
506D LEU* 3.9 32.8 - - + -
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Residues in contact with ARG 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D ALA* 3.3 1.8 - - + +
288D ILE* 1.3 81.3 - - + +
290D SER* 1.3 78.3 + - - +
292D PHE* 3.2 2.3 + - - +
293D GLU* 2.9 34.5 + - - +
311D LYS* 2.6 32.3 + - - +
312D LYS* 3.8 18.0 + - - +
313D VAL* 4.4 3.8 - - - +
501D TRP* 3.2 55.6 - - + +
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Residues in contact with SER 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D ALA* 3.5 20.6 + - - +
288D ILE 3.3 0.6 - - - -
289D ARG* 1.3 88.1 + - - +
291D ILE* 1.3 66.8 + - - +
293D GLU* 3.3 2.9 + - - +
294D GLU* 3.0 21.3 + - - +
312D LYS 4.8 4.2 + - - -
313D VAL* 4.0 27.1 - - - +
616D F89 3.8 31.2 + - - -
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Residues in contact with ILE 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D LEU* 4.4 0.9 - - + -
286D VAL* 3.9 14.8 - - + -
287D ALA 3.3 16.4 - - - +
288D ILE* 3.1 17.2 + - + +
290D SER* 1.3 75.5 - - - +
292D PHE* 1.3 64.1 + - - +
294D GLU* 3.0 16.7 + - - +
295D LEU* 3.0 12.6 + - + +
433D PHE* 3.4 30.3 - - + +
436D ALA* 3.4 27.1 - - + -
437D SER* 3.6 36.9 + - - +
440D ILE* 4.3 10.1 - - + -
616D F89 4.6 6.9 - - - -
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Residues in contact with PHE 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D ILE 2.9 11.8 + - - +
289D ARG 3.5 6.7 - - - +
291D ILE* 1.3 78.6 - - - +
293D GLU* 1.3 76.0 + - - +
295D LEU* 2.8 23.9 + - + +
296D ILE* 3.1 38.1 + - + +
440D ILE* 4.7 11.2 - - + +
444D MET* 3.7 26.9 - - + -
499D PHE* 3.7 8.5 - - + -
500D LYS* 3.4 12.8 - - - -
501D TRP* 3.2 53.8 - + + -
504D ILE* 3.2 27.6 - - + -
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Residues in contact with GLU 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D ARG* 2.9 30.7 + - + +
290D SER 3.7 4.3 - - - +
292D PHE* 1.3 93.5 - - - +
294D GLU* 1.3 59.1 + - - +
296D ILE* 2.7 40.7 - - + +
297D TRP* 3.2 9.4 - - - +
308D LEU* 4.0 7.8 - - + +
311D LYS* 3.3 55.3 + - + +
313D VAL* 3.8 14.1 - - + -
501D TRP* 4.5 8.1 - - - +
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Residues in contact with GLU 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D SER 3.0 10.7 + - - +
291D ILE* 3.0 10.9 + - - +
293D GLU* 1.3 75.5 - - - +
295D LEU* 1.3 59.5 + - - +
297D TRP* 3.1 12.5 - - + +
298D PHE* 3.0 55.4 + - + -
308D LEU* 4.0 11.6 - - + +
313D VAL* 5.2 0.4 - - + -
315D ILE* 3.2 19.3 - - + +
316D TRP* 2.8 30.4 + - + +
403D HIS* 5.6 1.1 + - - -
437D SER* 4.5 11.6 + - - -
615D UMP 5.6 0.4 - - - +
616D F89 3.3 25.6 + - + -
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Residues in contact with LEU 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D ILE* 3.0 10.9 + - + +
292D PHE* 2.8 12.6 + - + +
294D GLU* 1.3 74.1 - - - +
296D ILE* 1.3 60.3 + - - +
297D TRP 3.0 1.1 - - - -
298D PHE* 3.0 10.1 + - + +
299D ILE* 2.8 42.2 + - + +
346D TRP* 4.2 20.6 - - + -
437D SER* 3.6 24.7 + - - +
440D ILE* 3.6 21.3 - - + -
441D LEU* 3.5 39.3 - - + +
444D MET* 4.1 8.1 - - + -
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Residues in contact with ILE 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D PHE* 3.1 36.5 + - + +
293D GLU* 2.7 51.6 - - + +
295D LEU* 1.3 74.3 - - - +
297D TRP* 1.3 62.6 + - + +
299D ILE* 3.4 18.0 - - + +
300D LYS* 2.7 56.9 + - + +
311D LYS* 5.5 1.3 - - - +
444D MET* 4.7 0.9 - - + -
496D ILE 4.9 2.0 - - - +
497D GLU 4.8 9.0 - - - +
499D PHE* 3.6 31.9 - - + +
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Residues in contact with TRP 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D GLU 3.2 14.1 - - - +
294D GLU* 3.1 18.6 - - + +
296D ILE* 1.3 85.0 - - + +
298D PHE* 1.3 97.4 + + - +
300D LYS* 3.3 5.0 + - - +
301D GLY 3.3 1.7 + - - -
302D ASP* 3.1 69.1 + - + +
303D THR 3.7 22.2 - - - -
304D ASN 3.4 16.4 + - - -
305D GLY* 4.0 4.3 - - - -
307D HIS* 4.5 4.5 - - + -
308D LEU* 3.1 28.1 - - + +
316D TRP* 3.8 20.9 - + - -
338D LEU* 3.5 24.7 - - + -
341D ILE* 3.7 11.9 - - + -
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Residues in contact with PHE 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D GLU* 3.0 51.1 + - + -
295D LEU* 3.0 15.8 + - + +
297D TRP* 1.3 102.8 - + - +
299D ILE* 1.3 54.9 + - - +
301D GLY* 2.7 23.4 + - - -
302D ASP 4.9 0.9 - - - -
316D TRP* 4.3 3.6 - + - -
341D ILE* 5.0 0.7 - - + -
342D TYR* 3.5 50.3 - + + -
343D GLY* 3.3 16.6 - - - +
346D TRP* 3.6 32.7 - + + -
347D ARG* 4.3 0.7 - - - +
403D HIS* 3.8 20.0 - + - -
437D SER* 5.2 4.7 - - - -
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Residues in contact with ILE 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D LEU* 2.8 33.8 + - + +
296D ILE* 3.4 19.7 - - + +
298D PHE* 1.3 75.7 - - - +
300D LYS* 1.3 51.5 - - - +
301D GLY 3.4 0.7 + - - -
346D TRP* 4.1 10.3 - - + -
347D ARG* 2.7 36.8 + - - +
368D LEU* 3.7 23.8 - - + -
441D LEU* 4.4 4.3 - - + -
444D MET* 3.6 31.0 - - - -
496D ILE* 4.0 28.7 - - + +
497D GLU* 4.2 17.0 - - + -
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Residues in contact with LYS 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296D ILE* 2.7 45.5 + - + +
297D TRP* 3.5 8.3 - - - +
298D PHE 3.1 0.2 - - - -
299D ILE* 1.3 73.6 - - + +
301D GLY* 1.3 60.5 + - - +
302D ASP* 4.1 10.8 - - + +
347D ARG* 4.1 9.8 + - - +
348D HIS* 5.1 2.8 + - - -
497D GLU* 3.3 44.4 - - + +
499D PHE 5.6 1.1 - - - -
500D LYS* 5.7 5.8 - - - +
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Residues in contact with GLY 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D PHE 2.7 17.9 + - - -
299D ILE 3.2 0.6 - - - -
300D LYS* 1.3 73.8 - - - +
302D ASP* 1.3 63.2 + - - +
303D THR* 3.8 9.5 + - - +
343D GLY 3.3 26.2 - - - -
344D PHE* 4.2 7.8 - - - +
347D ARG* 3.6 10.3 - - - -
348D HIS* 4.5 9.7 + - - -
360D TYR* 6.1 0.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il